BIOL205 Lecture Notes - Lecture 1: Base Pair, Agarose Gel Electrophoresis, Gel Electrophoresis

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14 Feb 2017
Department
Course
Biology 205 Lab Notes
Overall Lab Objectives
1. Explain the relationships between DNA, RNA, proteins and traits.
2. Explain how PCR is used to amplify a specific DNA molecule.
3. Explain how genes, mRNA, coding sequences, open reading frames, and protein sequences are
related.
4. Compare and contrast in vivo DNA replication and PCR.
5. Use a molecular marker to identify alleles.
6. Use several bioinformatics resources and tools: OMIM, NCBI primerBLAST, Clustal Omega, ApE,
NCBI Gene, and GenBank.
7. Explain how meiosis gives rise to new genetic combinations.
8. Describe how agarose gel electrophoresis separates DNA fragments.
9. Use agarose gel electrophoresis to estimate DNA fragment sizes.
10. Analyse data to identify the important trends.
11. Communicate study findings in a scientific research report.
Who Killed Harriet Highbottom
1. Systematic Error = average mass in mg * Z correction factor
2. Random Error = standard deviation of at least 3 measurements
3. Z Correction Factor: Volume of water at 4 degrees C and standard atmospheric pressure
4. Table 1. ISO 8655 standards for micro-pipetting aids
5. Answer: We put six samples in the gel. 10 ml in each
lane from six places. Victim, suspects 1,2,3,4, and
crime scene. To find the person who killed Harriet, we
compared the DNA found at the crime scene. If there is
more than one that is the same as the crime scene then
we compared it to the victim.
SLC6A3 VNTR Allele Frequencies in a Population Sample-Week One
Learning Objectives
1. Find and interpret database records from GenBank
2. Use ApE to annotate DNA sequence
3. Explain the difference between a gene and a CDS
4. Explain why VNTR loci are used in forensic identification
5. Explain how agarose gel electrophoresis separates DNA fragments
6. Make a standard curve relating DNA fragment size to distance migrated on an agarose gel
7. Use a DNA migration standard curve to estimate DNA Fragment sizes
8. Use Excel to graphically compare allele frequencies
Preparation Questions
9. Why is it necessary to chelate the metal ions from solution during the boiling/lysis step at 100
degrees C? What would happen if you did not use a chelating agent such as the InstaGene
matrix?
10. What structures must be disrupted to release the DNA from a cell?
Bioinformatics analysis
11. Database searched: Genomic
Organisms searched: Arabidopsis thaliana
12. At a VNTR (variable number tandem repeat), locus, each distinct allele has a different physical
size because it has a different number of repeats. Thus, when we amplify an individuals
SLC6A3 VNTR locus, we can identify that individuals alleles by determining the size of the
PCR products produced.
Volume
Systematic
Error
Random
Error
500
microlitres
+/- 8
< 3
20
microlitres
+/- 1.6
< 0.6
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